Publications

Publications on Google Scholar and Pubmed Bibliography
 
2024
Single cell-transcriptomic analysis informs the lncRNA landscape in metastatic castration resistant prostate cancer.
Saha D, Dang HX, Zhang M, Quigley DA, Feng FY, Maher CA. span class="journal">NPJ Genomic Medicine. 2024 Feb 23;9(1):14. doi: 10.1038/s41525-024-00401-3.
Transcriptomic Heterogeneity of Expansile Cribriform and Other Gleason Pattern 4 Prostate Cancer Subtypes.
Chappidi MR, Sjöström M, Greenland NY, Cowan JE, Baskin AS, Shee K, Simko JP, Chan E, Stohr BA, Washington SL 3rd, Nguyen HG, Quigley DA, Davicioni E, Feng FY, Carroll PR, Cooperberg MR. Eur Urol Oncol.. 2024 Mar 19:S2588-9311(23)00120-7. doi: 10.1016/j.euo.2023.06.007
2023
Fragmentomic analysis of circulating tumor DNA-targeted cancer panels.
Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM, Bassetti M, Blitzer G, Floberg J, Sjöström M, Quigley DA, Dehm SM, Armstrong AJ, Beltran H, McKay RR, Feng FY, O'Regan R, Wisinski KB, Emamekhoo H, Wyatt AW, Lang JM, Zhao SG. Ann Oncol.. 2023 Sep;34(9):813-825. doi: 10.1016/j.annonc.2023.06.001. Epub 2023 Jun 16.
AARDVARK: An Automated Reversion Detector for Variants Affecting Resistance Kinetics
Moreno T, Magana J, Quigley DA
Bioinformatics. 2023 Aug 1;39(8):btad509. doi: 10.1093/bioinformatics/btad509
The genomic and epigenomic landscape of double-negative metastatic prostate cancer
Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, Gleave M, Lara PN, Reiter RE, Rettig MB, Witte ON, Wyatt AW, Feng FY*, Small EJ*, Quigley DA*
Cancer Research. 2023 Jun 8;CAN-23-0593. doi: 10.1158/0008-5472.CAN-23-0593
Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis.
Taylor MA, Kandyba E, Halliwill K, Delrosario R, Koroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam S, Mirzoeva O, Akhurst RJ, Balmain A.
bioRxiv. 2023 May 10:2023.05.08.539863. doi: 10.1101/2023.05.08.539863. Preprint
Reversible epigenetic alterations mediate PSMA expression heterogeneity in advanced metastatic prostate cancer.
Sayar E, Patel RA, Coleman IM, Roudier MP, Zhang A, Mustafi P, Low JY, Hanratty B, Ang LS, Bhatia V, Adil M, Bakbak H, Quigley DA, Schweizer MT, Hawley JE, Kollath L, True LD, Feng FY, Bander NH, Corey E, Lee JK, Morrissey C, Gulati R, Nelson PS, Haffner MC.
JCI Insight. 2023 Feb 23:e162907. doi: 10.1172/jci.insight.162907.
2022
Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity.
Westbrook TC, Guan X, Rodansky E, Flores D, Liu CJ, Udager AM, Patel RA, Haffner MC, Hu YM, Sun D, Beer TM, Foye A, Aggarwal R, Quigley DA, Youngren JF, Ryan CJ, Gleave M, Wang Y, Huang J, Coleman I, Morrissey C, Nelson PS, Evans CP, Lara P, Reiter RE, Witte O, Rettig M, Wong CK, Weinstein AS, Uzunangelov V, Stuart JM, Thomas GV, Feng FY, Small EJ, Yates JA, Xia Z, Alumkal JJ.
Nat Commun. 2022 Sep 15;13(1):5345. doi: 10.1038/s41467-022-32701-6.
Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.
O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A.
Cancer Res. 2022 Oct 23:OF1-OF12. doi: 10.1158/0008-5472.CAN-21-4335.
Intrinsic Molecular Subtypes of Metastatic Castration-Resistant Prostate Cancer.
Feng E, Rydzewski NR, Zhang M, Lundberg A, Bootsma M, Helzer KT, Lang JM, Aggarwal R, Small EJ, Quigley DA, Sjöström M, Zhao SG.
Clin Cancer Res. 2022 Oct 19:CCR-22-2567. doi: 10.1158/1078-0432.CCR-22-2567.
Why ARNT Prostate Tumors Responding to Enzalutamide?
Zhang M, Moreno-Rodriguez T and Quigley D
Cancer Discovery 2022 Sep 2;12(9):2017-2019. doi: 10.1158/2159-8290.CD-22-0702.
Commentary on Linder et al. Cancer Discovery 2022
The 5-hydroxymethylcytosine landscape of prostate cancer
Sjöström M, Zhao SG, Levy S ... He H, Wyatt A#, Quigley D#, and Feng FY#.
Cancer Research 2022 Oct 17:OF1-OF15. doi: 10.1158/0008-5472.CAN-22-1123
Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer.
Herberts C, Annala M, Sipola J, Ng SWS, Chen XE, Nurminen A, Korhonen OV, Munzur AD, Beja K, Schönlau E, Bernales CQ, Ritch E, Bacon JVW, Lack NA, Nykter M, Aggarwal R, Small EJ, Gleave ME; SU2C/PCF West Coast Prostate Cancer Dream Team, Quigley DA, Feng FY#, Chi KN#, Wyatt AW#.
Nature 2022 Jul 20. doi: 10.1038/s41586-022-04975-9
Androgen receptor reprogramming demarcates prognostic, context-dependent gene sets in primary and metastatic prostate cancer.
Severson T, Qiu X, Alshalalfa M, Sjöström M, Quigley D, Bergman A, Long H, Feng F, Freedman ML, Zwart W, Pomerantz MM.
Clin Epigenetics 2022 May 4;14(1):60. doi: 10.1186/s13148-022-01278-8.
2021
Prognosis Associated With Luminal and Basal Subtypes of Metastatic Prostate Cancer.
Aggarwal R, Rydzewski NR, Zhang L, Foye A, Kim W, Helzer KT, Bakhtiar H, Chang SL, Perry MD, Gleave M, Reiter RE, Huang J, Evans CP, Alumkal JJ, Lang JM, Yu M, Quigley DA, Sjöström M, Small EJ, Feng FY, Zhao SG
JAMA Oncology 10.1001/jamaoncol.2021.3987
The largest integrated clinical, transcriptomic, and genomic analysis of mCRPC samples to date suggests that mCRPC can be classified as luminal and basal tumors.
Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures.
Rydzewski NR, Peterson E, Lang JM, Yu M, Laura Chang S, Sjöström M, Bakhtiar H, Song G, Helzer KT, Bootsma ML, Chen WS, Shrestha RM, Zhang M, Quigley DA, Aggarwal R, Small EJ, Wahl DR, Feng FY, Zhao SG
NPJ Genomic Medicine 10.1038/s41525-021-00239-z
An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer.
Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA
Nature Communications 10.1038/s41467-021-24919-7
CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer.
Ahmed M, Soares F, Xia JH, Yang Y, Li J, Guo H, Su P, Tian Y, Lee HJ, Wang M, Akhtar N, Houlahan KE, Bosch A, Zhou S, Mazrooei P, Hua JT, Chen S, Petricca J, Zeng Y, Davies A, Fraser M, Quigley DA, Feng FY, Boutros PC, Lupien M, Zoubeidi A, Wang L, Walsh MJ, Wang T, Ren S, Wei GH, He HH
Nature Communications 10.1038/s41467-021-21867-0
2020
One of These Things is Not Like the Others: Targeting ATM-mutant Prostate Cancer.
Quigley DA
European Urology 10.1016/j.eururo.2020.11.018
Commentary on Neeb et al. European Urology 2020
SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression.
Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA
Scientific Reports 10.1038/s41598-020-71168-7
Autoantibody Landscape in Patients with Advanced Prostate Cancer.
Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, , Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY
Clinical Cancer Research 10.1158/1078-0432.CCR-20-1966
Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer.
Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P Jr, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, , Quigley DA, Foye A, Chen WS, Youngren J, Weinstein AS, Stuart JM, Feng FY, Small EJ, Xia Z, Alumkal JJ
Clinical Cancer Research 10.1158/1078-0432.CCR-19-2303
The DNA methylation landscape of advanced prostate cancer
Zhao SG*, Chen WS*, Li H*, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT,, Barnard TJ, Bailey AM, Chow E, Perry M, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M,, Chang SL, Houlahan KE, Shiah Y, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB,, Witte O, Kim MY, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H,, Asangani IA, Sandhu S, Lang JM, Mahajan N, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH,, Huang J, Zwart W, Costello JF, Luo J, Tomlins SW, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM#, Maher CA#, Small EJ#, Quigley DA#, Feng FY#
Nature Genetics 10.1038/s41588-020-0648-8. Epub 2020 Jul 13
We performed whole genome methylation analysis of 100 metastatic prostate tumors, extending our investigation of the cohort we published in (Quigley et al Cell 2018). We observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2, DNMT3B, IDH1 and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions.
Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer.
Kwon DH, Zhang L, Quigley DA, Foye A, Chen WS, Wong CK, Feng FY, Bailey A, Huang J, Stuart JM, Friedl V, Weinstein AS, Beer TM, Alumkal JJ, Rettig M, Gleave M, , Lara PN Jr, Thomas GV, Li P, Lui A, Small EJ, Aggarwal RR.
Urologic Oncology 10.1016/j.urolonc.2020.06.002
Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance.
Alumkal JJ, Sun D, Lu E, Beer TM, Thomas GV, Latour E, Aggarwal R, Cetnar J, Ryan CJ, Tabatabaei S, Bailey S, Turina CB, Quigley DA, Guan X, , Foye A, Youngren JF, Urrutia J, Huang J, Weinstein AS, Friedl V, Rettig M, Reiter RE, Spratt DE, Gleave M, Evans CP, Stuart JM, Chen Y, , Feng FY, Small EJ, Witte ON., Xia Z
Proc Natl Acad Sci U S A. 10.1073/pnas.1922207117
An integrated molecular profile of endometrioid ovarian cancer
Pierson WE, Peters PN, Chang MT, Chen L, Quigley DA, Ashworth A,, Chapman JS
Gynecologic Oncology 2020 Apr;157(1):55-61. doi: 10.1016/j.ygyno.2020.02.011
Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy
Chou J, Quigley DA, Robinson TM, Feng FY,, Ashworth A
Cancer Discovery 2020 Feb 18. doi: 10.1158/2159-8290.CD-19-0528.
Reviews the roles of CDKs in cancer, with a focus on CDK12.
Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer
Li Y, Yang R, Henzler CM, Ho Y, Passow C, Auch B, Carreira S, Nava Rodrigues D, Bertan C, Hwang TH, Quigley DA, Dang HX,, Morrissey C, Fraser M, Plymate SR, Maher CA, Feng FY, de Bono JS, Dehm SM
Clinical Cancer Research 2020 Jan 13. doi: 10.1158/1078-0432.CCR-19-3023
Work led by Scott Dehm's lab that investigated how AR gene rearrangements contribute to endocrine therapy resistance in castration-resistant prostate cancer.
2019
Prostate cancer research: The next generation; report from the 2019 Coffey‐Holden Prostate Cancer Academy Meeting
Miyahira AK, Sharp A, Ellis L, Jones J, Kaochar S, Larman HB, Quigley DA, Ye H, Simons JW, Pienta KJ, Soule HR
The Prostate 2019 Dec 11. doi: 10.1002/pros.23934
Summarizes research presented at the 2019 PCF Coffey-Holden meeting.
Niche-Specific Factors Dynamically Regulate Sebaceous Gland Stem Cells in the Skin
Veniaminova NA, Grachtchouk M, Doane OJ, Peterson JK, Quigley DA, Lull MV, Pyrozhenko DV, Nair RR,, Patrick MT, Balmain A, Dlugosz AA, Tsoi LC, Wong SY
Developmental Cell 2019 Nov 4;51(3):326-340.e4. doi: 10.1016/j.devcel.2019.08.015.
DNA-dependent protein kinase drives prostate cancer progression through transcriptional regulation of the Wnt signaling pathway
Kothari V, Goodwin J, Zhao S, Drake J, Yin Y, Chang L, Evans J, Wilder-Romans K, Gabbara K, Dylgjeri E, Chou J, Sun G, Tomlins S,, Hege R, Kristen , Filvaroff E, Schaeffer EM, Karnes RJ, Quigley DA, Rathkopf D, Hansen H ,, Speers C, Spratt D, Gilbert L, Ashworth A, Chinnaiyan A, Raj G, Knudsen K, Feng FY
Clinical Cancer Research 2019 Sep 15;25(18):5608-5622. doi: 10.1158/1078-0432.CCR-18-2387.
Novel RB1-loss transcriptomic signature is associated with poor clinical outcomes across cancer types
Chen WS*, Alshalalfa M*, Zhao SG, Liu Y, Mahal B, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL#, Feng FY#
Clinical Cancer Research 2019 Apr 22. pii: clincanres.0404.2019. doi: 10.1158/1078-0432.CCR-19-0404.
We developed a transcriptomic signature of biallelic RB1 loss and demonstrate RB1 loss is associated with shorter survival in Pan-cancer and in mCRPC.
Genomic drivers of poor prognosis and enzalutamide resistance in metastatic castration-resistant prostate cancer
Chen WS, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley DA, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D,, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, Xia Z, Chi KN, Reiter RE, Maher CA, Feng FY, Small EJ, Alumkal JJ, on behalf of the West Coast Prostate Cancer Dream Team
European Urology 2019 Mar 27. pii: S0302-2838(19)30206-4. doi: 10.1016/j.eururo.2019.03.020
We used whole genome and transcriptome analysis of men with advanced prostate cancer to demonstrate that biallelic loss of RB1 is independently associated with poor overall survival among men with mCRPC. WNT pathway deregulation is assocaited with enzalutamide resistance in these patients.
Whole Genome and Transcriptional Analysis of Treatment-Emergent Small Cell Neuroendocrine Prostate Cancer Demonstrates Intra-Class Heterogeneity
Aggarwal R*, Quigley DA*, Huang J, Zhang L, Beer T, Rettig M, Reiter R, Gleave M, Thomas G, Foye A, Denis Playdle, Lloyd P, Chi K, Evans C, Lara P, Feng FY#, Alumkal J#, Small EJ#
Molecular Cancer Research 2019 Mar 27. pii: molcanres.1101.2018. doi: 10.1158/1541-7786.MCR-18-1101.
Using an expression-based definition of t-SCNC, we found t-SCNC tumors were significantly less likely to have amplification of AR or an intergenic AR-enhancer locus. These t-SCNC tumors demonstrated both inter- and intra-individual heterogeneity, in particular with respect to neuroendocrine markers.
High density is a property of slow-cycling and treatment-resistant human glioblastoma cells
Sabelström H,, Quigley DA, Fenster T, Foster DJ, Fuchshuber CAM, Saxena S, Yuan E, Li N, Paterno F, Phillips JJ, James CD, Norling B, Berger MS, Persson AI
Experimental Cell Research 2019 Mar 5. pii: S0014-4827(19)30091-6. doi: 10.1016/j.yexcr.2019.03.003
2018
A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS
McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, Chen B, Quigley DA, Luk JM, Kelley RK,, Gordan JD, Gill RM, Blanchard SB, Ruggero D
eLife 2019 Sep 3;8. pii: e48847. doi: 10.7554/eLife.48847.
DNA Repair Gene Alterations and PARP Inhibitor Response in Patients With Metastatic Castration-Resistant Prostate Cancer
Lu E, Thomas GV, Chen Y, Wyatt AW, Lloyd P, Youngren J, Quigley D, Bergan R, Bailey S, Beer TM, Feng FY, Small EJ, Alumkal JJ
J Natl Compr Canc Network 2018 Aug;16(8):933-937. doi: 10.6004/jnccn.2018.7020
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
Quigley DA*, Dang H*, Zhao SG*, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V,, Perry M, Bailey A, Playdle D, Barnard T, Zhang L, Zhang J, Youngren J, Cieslik M, Parolia A,, Beer T, Thomas G, Chi K, Gleave M, Lack A, Zoubeidi A, Reiter R, Rettig M, Witte O, Ryan C,, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H,, Gilbert L, Lara P, Evans C, Goldstein T, Stuart J, Tomlins S, Spratt D, Cheetham RK, Cheng D,, Farh K, Gehring J, Hakenberg J, Liao A, Febbo P, Shon J, Sickler B, Batzoglou S, Knudsen KE,, He H, Huang J, Wyatt A, Dehm S, Ashworth A, Chinnaiyan A#, Maher CA#, Small EJ#, Feng FY#
Cell 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039
We performed integrated analysis of DNA and RNA from 101 metastatic prostate cancer whole genomes. We show an enhancer region affects the Androgen Receptor in approximately 80% of mCRPC and demonstrated how DNA repair defects associated with loss of BRCA2, CDK12, and TP53 are associated with genomic scars of deletions, tandem duplication, and chromothripsis.
summary genomic data, raw genomic data.
Nature News and Views
Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry
Gonzalez V, Samusik N, Chen T, Savig E, Aghaeepour A, Quigley DA, Huang Y, Giangarra V, Borowsky A, Hubbard N, Chen S, Han G,, Ashworth A, Kipps T, Berek J, Nolan G, Fantl W
Cell Reports 2018 Feb 13;22(7):1875-1888. doi: 10.1016/j.celrep.2018.01.053
Antisecretory Factor-mediated Inhibition of Cell Volume Dynamics Produces Anti-tumor Activity in Glioblastoma
Ilkhanizadeh S, Sabelström H, Miroshnikova Y, Frantz A, Zhu W, Idilli A, Lakins J, Schmidt C, Quigley D, Fenster T, Yuan E, Trzeciak J, Saxena S, Lindberg O , Mouw J, Burdick J, Magnitsky S, Berger M, Philips J, Arosio D, Sun S, Weaver V, Weiss WA, Persson A
Molecular Cancer Research 2018 Feb 5. pii: molcanres.0413.2017. doi: 10.1158/1541-7786.MCR-17-0413
2017
Analysis of circulating cell-free DNA identifies multi-clonal heterogeneity of BRCA2 reversion mutations associated with resistance to PARP inhibitors
Quigley DA*, Alumkal JJ*, Wyatt A, Kothari V, Foye A, Lloyd P, Aggarwal R, Kim W, Lu E, Schwartzman J, Beja K, Annala M, Das R, Diolaiti M, Pritchard C, Thomas G, Tomlins S, Knudsen K, Lord C, Ryan C, Youngren J, Beer T, Ashworth A#, Small E#, Feng FY#
Cancer Discovery 2017 Sep;7(9):999-1005. doi: 10.1158/2159-8290.CD-17-0146.
We demonstrated that a common form of PARP inhibitor resistance, called reversion mutations, can be detected in advanced prostate cancer by liquid biopsy. We employed deep sequencing of pre- and post-resistance DNA from patients with advanced prostate cancer who progressed on two different PARP inhibitors. We showed that resistance arises many times independently in different cells.
Age, estrogen, and immune response in breast adenocarcinoma and adjacent normal tissue
Quigley DA, Tahiri A, Lüders T, Riis M, Balmain A, Børresen-Dale A, Bukholm I, Kristensen V
OncoImmunology 2017 Aug 10;6(11):e1356142. doi: 10.1080/2162402X.2017.1356142
We performed gene expression analysis of 200 breast adenocarcinomas with matched adjacent normal tissue.
Raw microarray data can be downloaded from GEO GSE70947, GEO GSE70947, GEO GSE70951
Code and data to reproduce this analysis
2016
Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer
Halliwill K, Quigley DA, Kang HC, Rosario R, Ginzinger D, Balmain A
Genome Medicine 2016 Aug 9;8(1):83.
Large Scale Profiling of Kinase Dependencies in Cancer Cell Lines
Campbell J, Ryan C, Brough R, Bajrami I, Pemberton H, Chong I, Costa-Cabral S, Frankum J,, Gulati A, Holme H, Miller R, Postel-Vinay S, Rafiq R, Wei W, Williamson C, Quigley DA,, Tym J, Al-Lazikani B, Fenton T, Natrajan R, Strauss S, Ashworth A, Lord C
Cell Reports 2016 Mar 15;14(10):2490-501
Gene expression architecture of mouse dorsal and tail skin reveals functional differences in inflammation and cancer
Quigley DA, Kandyba E, Huang P, Halliwill K, Sjölund J, Pelorosso F, Wong C, Hirst G, Wu D, Delrosario R, Kumar A, Balmain A
Cell Reports 2016 Jul 26;16(4):1153-65.
Here we mapped the genetic architecture of skin perturbed by genetics, inflammation, and tumorigenesis.
Code and data to reproduce these analyses.
2015
Predicting prognosis and therapeutic response from interactions between lymphocytes and tumor cells
Quigley DA, Kristensen V
Molecular Oncology 2015 Dec;9(10):2054-62.
equalizer reduces SNP bias in Affymetrix microarrays
Quigley DA
BMC Bioinformatics 2015, 16:238 (30 July 2015)
The software package equalizer allows you to remove probes from Affymetrix microarrays using VCF files that describe the location of germline SNPs. See the equalizer project page for more information.
2014
Expression Quantitative Trait Loci and Receptor Pharmacology Implicate Arg1 and the GABA-A Receptor as Therapeutic Targets in Neuroblastoma
Hackett C, Quigley DA, Wong R, Chen J, Cheng C, Song Y, Wei J, Pawlikowska L, Bao Y,, Goldenberg D, Nguyen K, Gustafson W, Rallapalli S, Cho Y, Cook J, Kozlov S, Mao J, Van Dyke T,, Kwok P, Kahn J, Balmain A, Fan Q, Weiss W
Cell Reports 2014 Nov 6;9(3):1034-46
The mutational landscapes of genetic and chemical models of Kras-driven non-small cell lung cancer
Westcott PM, Halliwill KD, To M, Mamunar R, Rust A, Keane T, Delrosario R, Jen K, Fredlund E, Quigley DA, Gurley K, Kemp C, Adams D, Balmain A
Nature 2014 Nov 2. doi: 10.1038/nature13898.
TP53 mutation spectrum in breast cancer is subtype specific and has distinct prognostic relevance
Silwal-Pandit L, Vollan HK, Chin SF, Rueda OM, McKinney S, Osako T, Quigley DA,, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Langerød A
Clinical Cancer Research 2014 Jul 1;20(13):3569-80.
Lung Tumorigenesis in a Conditional Cul4A Transgenic Mouse Model
Yang YL, Hung MS, Wang Y, Ni J, Mao JH, Hsieh D, Au A, Kumar A, Quigley D, Fang LT, Yeh CC, Xu Z, Jablons DM, You#, L#
Journal of Pathology 2014 Mar 19.
The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors
Quigley DA, Fiorito E, Nord S, Van Loo P, Alnaes G, Fleischer T, Tost J,, Vollan HK, Tramm T, Overgaard J, Bukholm IR, Hurtado A, Balmain A, Börresen-Dale A,, Kristensen V
Molecular Oncology 2014 Mar;8(2):273-84
Here we used eQTL mapping and functional analysis in normal breast tissue and breast tumors to propose a mechanism for the breast cancer susceptibility locus on 5p12, previously identified by GWAS.
Identification of Hipk2 as an essential regulator of white fat development
Sjölund J, Pelorosso F, Quigley DA, DelRosario R, Balmain A
Proceedings of the National Academy of Sciences 2014 May 20;111(20):7373-8
2013
Rewiring of human lung cell lineage and mitotic networks in lung adenocarcinomas
Kim IJ, Quigley D, To M, Jen, Pham P, Lin K, Jo B, Jen K, Raz D, Kim J, Mao JH, Jablons D, Balmain A
Nature Communications 2013 Apr 16.
Inflammation and Hras Signaling Control Epithelial-mesenchymal Transition during Skin Tumor Progression
Wong C, Yu J, Quigley DA, To M, Jen Kuang-Yu, Huang P, Del Rosario R, Balmain A
Genes and Development 2013 Mar 15;27(6):670-82
Multiple Self-Healing Squamous Epithelioma (MSSE): Rare Variants in an Adjacent Region of Chromosome 9q22.3 to known TGFBR1 Mutations Suggest a Digenic or Multilocus Etiology
Kang HC, Quigley D, Kim IJ, Wakabayashi Y, Ferguson-Smith MA, D'Alessandro M, Lane EB, Akhurst RJ, Goudie DR, Balmain A
Journal of Investigative Dermatology 2013 January 28.
2012
Mouse and human strategies identify PTPN14 as a modifier of angiogenesis and hereditary haemorrhagic telangiectasia
Benzinou M, Clermont FF, Letteboer TG, Kim JH, Espejel S, Harradine KA, Arbelaez J, Luu MT, Roy R, Quigley D, Higgins MN, Zaid M,, Aouizerat BE, van Amstel JK, Giraud S, Dupuis-Girod S, Lesca G, Plauchu H, Hughes CC, Westermann CJ, Akhurst RJ
Nature Communications 2012 January 10.
2011
Progressive genomic instability in the FVB/KrasLA2 mouse model of lung cancer
To MD, Quigley D, Mao J, Rosario R, Hsu J, Hodgson G, Jacks T, Balmain A
Molecular Cancer Research 2011 August 1
Network Analysis of Skin Tumor Progression Identifies a Rewired Genetic Architecture Affecting Inflammation and Tumor Susceptibility
Quigley DA, To MD, Kim IJ, Lin KK, Albertson DG, Sjolund J, Perez-Losada J, Balmain A
Genome Biology 2011 Jan 18;12(1):R5.
Here we show how the genetic architecture of skin cancer is affected by somatic alterations during progression from normal tissue through benign and malignant tumors. Raw expression and array-CGH data are available in GEO in SuperSeries GSE21264.
Membrane Array Analysis of Tear Proteins in Ocular Cicatricial Pemphigoid
Chan MF, Sack R, Quigley DA, Sathe S, Vijmasi T, Li S, Holsclaw D, Strauss EC,, McNamara NA
Optometry & Visual Science 2011 May 5
Amphotericin B and natamycin are not synergistic in vitro against Fusarium and Aspergillus spp. isolated from keratitis
Lalitha P, Shapiro BL, Loh AR, Fothergill AW, Prajna NV, Srinivasan M, Oldenburg CE, Quigley DA, Chidambaram JD, McLeod SD, Acharya NR, Lietman TM
British Journal 2011 May;95(5):744-5
Outgrowth of drug-resistant carcinomas expressing markers of tumor aggression after long-term TGFBRI/II kinase inhibition with LY2109761
Connolly EC, Saunier EF, Quigley D, Luu MT, De Sapio A, Hann B, Yingling JM, Akhurst RJ
Cancer Research 2011 Mar 15;71(6):2339-49
2010
Deletion of the PER3 gene on chromosome 1p36 in recurrent ER-positive breast cancer
Climent J, Perez-Losada J, Quigley DA, Kim IJ, Delrosario R, Jen KY, Bosch A, Lluch A, Mao JH, Balmain A
Journal 2010. Aug 10;28(23):3770-8
2009
Systems genetics analysis of cancer susceptibility: from mouse models to humans
Quigley DA, Balmain A
Nature Reviews: Genetics 2009. Sep;10(9) 651-7.
This Perspective reviewed the state of systems genetics analysis of cancer.
Genetic architecture of mouse skin inflammation and tumor susceptibility
Quigley DA, To MD, Perez-Losada J, Pelorosso F, Mao J, Nagase H, Ginzinger D, Balmain A
Nature 2009. Mar 26;458(7237):505-8.
Here we used eQTL mapping in normal skin of mice who had developed tumors to define the genetic architecture of normal tissue and identify loci associated with hematopoietic traits and tumor development
2008
Antibody Protein Array Analysis of the Tear Film Cytokines
Li S, Sack R, Vijmasi T, Sathe S, Beaton A, Quigley D, Gallup M, McNamara N
Optometry & Vision Science 2008. Aug;85(8):653-60
2007
Learning regulatory programs that accurately predict differential expression with MEDUSA
Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L,, Leslie C
Ann N Y Acad Sci. 2007 Dec;1115:178-202
Updated July 2022